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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of human acute appendicitis

ABSTRACT: Gene expression was evaluated in 9 appendix samples removed from patients who went to the operating room with the diagnosis of acute appendicitis and 4 samples removed for non-inflammatory reasons. A circumferential piece of tissue was obtained at the distal aspect of each specimen. The tissue was flash frozen at -80 degrees for later processing. Frozen specimens were homogenized into TriReagent and RNA was isolated according to the manufacturerâs instruction. RNA was processed and hybridized to Affymetrix microarray. Experiment Overall Design: 9 patients and 4 controls

ORGANISM(S): Homo sapiens

SUBMITTER: Bruce Horwitz

PROVIDER: E-GEOD-9579 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Gene Expression in Acute Appendicitis

Project description:Gene expression was evaluated in 9 appendix samples removed from patients who went to the operating room with the diagnosis of acute appendicitis and 4 samples removed for non-inflammatory reasons. A circumferential piece of tissue was obtained at the distal aspect of each specimen. The tissue was flash frozen at -80 degrees for later processing. Frozen specimens were homogenized into TriReagent and RNA was isolated according to the manufacturer's instruction. RNA was processed and hybridized to Affymetrix microarray. Keywords: Disease state analysis

2008-04-22 | GSE9579 | GEO

miRNA experiment of fresh frozen colonic biopsy samples

Project description:The aim of the present study was to perform an additional global miRNA microarray analysis of tubular and tubulovillous adenoma biopsy specimen completed with colorectal adenocarcinomas using fresh frozen tisse

2016-10-19 | GSE83924 | GEO

Left ventricular samples from humans with ischemic heart failure and non-failing controls

Project description:LCMS files from tryptic digests of ~1-4 mg piece of heart ventricular tissue from human with ischemic heart failure and non-failing controls. Specimen number correspond to .raw files as follows: Ischemic Heart failure - 54687.1; HF_1_phos.raw 53148.1; HF_2_phos.raw 53589.2; HF_3_phos.raw 54146.1; HF_4_phos.raw 52935.1; HF_5_phos.raw Non-failing - 52941.1; NHF_1_phos.raw 52777.1; NHF_2_phos.raw 53019.2; NHF_3_phos.raw 53058.1; NHF_4_phos.raw 52621.1; NHF_5_phos.raw

2022-12-07 | MSV000090858 | MassIVE

An oncogenic Kras expression signature identified by cross-species

Project description:Mouse lung cancers were generated using the KrasLA model, in which a latent mutated Kras2 allele (resulting in the amino acid substitution G12D) is sporadically activated through spontaneous homologous recombination. These mice develop lung adenomas with full penetrance; over time, the tumors acquire morphologic characteristics reminiscent of those of human adenocarcinoma, such as nuclear atypia and a high mitotic index. KrasLA2 mice on a 129svJae background were crossed with wild type C57B/6J mice to obtain F1 progeny. The initial report of this mouse model described two alleles, KrasLA1 and KrasLA2. All expression profiles in this study were generated using the KrasLA2 mice. We call the model KrasLA throughout for simplicity. Mice bearing the KrasLA latent allele were allowed to develop to 5-6 month of age and sacrificed by cervical dislocation. Lungs were removed and placed in RNAlaterTM solution (Ambion). Individual tumors large enough to be easily dissected (3mm-8mm) were removed and cut into 2 pieces. One piece was placed in formalin to be used for histological analysis while the other piece was stored at -80 for RNA/DNA extraction.

2013-08-01 | GSE49200 | GEO

Removed

Project description:Removed

| PRJEB28844 | ENA

Expression data from melanosis coli (MC)

Project description:There is still a big debate about the correlation between melanosis coli (MC) and carcinoma. We used HTA2.0 to investigate the expression changes of lncRNAs and mRNAs in human colonic mucosa with or without MC and try to investigate MC from gene aspect, eventually to demonstrate whether thereâs a certain correlation between MC and carcinoma. GeneChipÂ® Human Transcriptome Array 2.0 (HTA 2.0) microarrays were adopted. The expression profile of lncRNAs and mRNA were tested in five colon tissue biopsy specimen of MC patients and five demographically-matched controls. This study recruited a total of five MC patients and five coupled matched controls. All specimens were obtained from colonoscopy. The fresh specimens of colon tissues form MC patients and control patients were washed with RNAase free water and put into RNAlater (Qiagen) immediately and frozen in -80Â°C. Gene Ontology (GO) and KEGG Pathway analyses of aberrantly expressed mRNAs were performed to identify the related biological functions and pathologic pathways.

2016-05-30 | E-GEOD-78933 | biostudies-arrayexpress

Appendix metagenome

Project description:Appendix Metagenome

| PRJNA596776 | ENA

Effect of oestrogen treatment on growth of human angiomyolipoma xenograft tumours

Project description:SV7tert AML cells were obtained from ATCC and cultured in Dulbecco's modified essential medium (DMEM), glutamine (4mmol) and 10% foetal bovine serum (FBS). Two million SV7tertAML cells were subcutaneously injected into nude mice either with or without subcutaneous oestrogen pellets (n=4 per group); oestrogen was added using 0.36mg 60 day release oestrogen pellets implanted sub-cutaneously. Mice were housed in pathoflex isolators at 26°C, on 12 hour light / dark cycles. Irradiated RB2 diet and autoclaved water provided ad libertum. All oestrogen treated mice inoculated with SV7tertAML cells developed subcutaneous tumours which required termination of the animals at six weeks due to tumour load. These primary tumours were removed and fragments placed subcutaneously in further nude mice which went on to develop tumours both in the presence and absence of oestrogen. Mice were weighed weekly and their clinical condition closely monitored by a trained observer. Mice were terminated individually when the tumour cross-sectional area reached 250mm2 or sooner, which has previously been seen to be below the limit of 10% of initial body weight set by the UKCCCR guidelines. Tumours were removed and a portion flash frozen in liquid nitrogen. RNA was extracted from five tumours from oestrogen treated and control animals. Equal quantities of RNA was pooled and quality checked by Agilent Bioanylyser. Experimenter name = Simon Johnson Experimenter institute = Queens Medical Centre Keywords: estrogen treatment, angiomyolipoma xenograft tumors

2007-09-19 | GSE5868 | GEO

Partial urethra obstruction in rat

Project description:Urethra was partially ligated and the urinary bladder was removed 10 days or 6 weeks after obstruction. Sham operated rats were used as controls. An addtitonal group of rats were repoerated 6 weeks after surgery and the obstruction was removed. These rats were then sacrificed 10 days after deobstruction. The bladder (including the urothelium) was frozen and used for RNA extraction.

2013-11-24 | GSE47080 | GEO

Epigenetic inactivation of the autophagy-lysosomal system in the Parkinson’s disease appendix (2: PD_RNASeq)

Project description:The gastrointestinal tract may be a site of origin for α-synuclein (α-syn) pathology in idiopathic Parkinson’s disease (PD), and an abundance of aggregated α-syn has recently been demonstrated in both the healthy and PD appendix. However, the molecular changes that enable gut α-syn aggregates to contribute to the development and progression of PD remain unclear. Here, our deep-sequencing of DNA methylation changes at 521 autophagy-lysosomal pathway (ALP) genes in the human appendix and brain in PD and healthy controls indicates a pattern of widespread hypermethylation in the PD appendix that is recapitulated in the PD brain. There is significant overlap in the individual ALP genes affected across the PD appendix and brain, with lysosomal genes specifically downregulated in both regions. Healthy epigenetic aging, which involves a hypermethylation of macroautophagy and selective autophagy genes in the appendix and brain, is disrupted in both areas in PD. In mice, DNA methylation changes at ALP genes induced by chronic gut inflammation are greatly exacerbated by the presence of α-syn pathology. DNA methylation changes at ALP genes induced by α-synucleinopathy are significantly associated with the ALP abnormalities observed in the PD appendix, specifically involving lysosomal genes. Our work, which constitutes an in-depth, unbiased investigation of epigenetic changes in the ALP of the PD gut and brain, identifies the epigenetic misregulation of the ALP, especially a downregulation of lysosomal genes, as a potential culprit for the initiation and spread of α-syn pathology in idiopathic PD.

2021-02-01 | GSE135743 | GEO

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